Internal

Objetos usados solo en las viñetas.

interpro_INTERPRO_long

interpro_INTERPRO_long

interpro_INTERPRO_profile

interpro_INTERPRO_profile

interpro_KEGG_long

interpro_KEGG_long

interpro_map

interpro_map

interpro_pfam_long

interpro_pfam_long

interpro_pfam_profile

interpro_pfam_profile

ko_bin_mapp

Output of mapping_ko

ko_bin_table

Output of read_ko

metadata

Metadata

rbims

Main Rbims

read_ko_shiny()

Read the output of KofamScan/KofamKoala or KAAS.

KEGG analysis

Functions used for KEGG

read_ko()

Read the output of KofamScan/KofamKoala or KAAS.

mapping_ko()

Maps KOs to the KEGG database.

read_picrust2()

Read the output of PICRUSt2

write_metabolism()

Metabolism table

InterProScan analysis

Functions used for InterProScan analysis

read_interpro()

Extract abundance profile of InterProScan output.

MEROPS analysis

Functions used for MEROPS analysis

read_merops()

Read the output of merops and extract abundance profile

dbCAN analysis

Functions used for dbCAN analysis

read_dbcan3()

Read the output of dbCAN and extract abundance profile

Manipulate KEGG/InterproScan profile

Functions used to manipulate the KEGG/InterproScan profile

get_subset_unique()

Unique abundance profile.

get_subset_pca()

Metabolism PCA.

get_subset_pathway()

Subsets the mapped KO table based on pathways.

calc_binary()

Calculate presence/absence.

calc_percentage()

Calculate the percentage.

Plot KEGG/InterproScan profile

Functions used to plot the KEGG/InterproScan profile

plot_bubble()

Bubble plot.

plot_heatmap()

Heatmap